did a bunch of work to the new main plot.sh script

plot.sh

@@ -3,3 +3,54 @@
 # This metascript uses the available plotting scripts to produce a list of
 # document-rady plots.
 
+# Only analyses with this error type will be represented in the atlas
+errtype="CM"
+ref_band="1367Å"
+echo_bands=$(ls analyses/*CM*|sed 's|[^≺]*≺_\(.\{5\}\).*|\1|')
+
+# echo Using list of reverberated bands: $echo_bands
+
+echo Propagating tables.
+scripts/propagate_tables.sh > /dev/null
+
+case $1 in
+    "PSD")
+        echo "Producing PSD atlas."
+        gnuplot_file=psd_atlas.gp
+        gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n|␤|g')
+        for tabfile in analyses/tables/PSD_*${errtype}*;
+        do
+            echo_band=$(basename $tabfile|
+                        sed 's|PSD[_ ]\(.\{5\}\)[_ ]{[^_ ]*}.tab|\1|')
+            if [[ "$echo_band" == "$ref_band" ]] ; then continue; fi
+            gnuplot_input_edit=$(echo "$gnuplot_input"|
+                                    sed "s|%FILE%|$tabfile|"|
+                                    sed "s|%LABEL%|$echo_band|")
+            gnuplot_input="${gnuplot_input_edit}"
+        done
+        echo "$gnuplot_input"|perl -pe 's|␤|\n|g' > ${gnuplot_file}
+        gnuplot $gnuplot_file
+
+    ;;
+
+    "lags")
+        echo "Producing time delay atlas."
+        gnuplot_file=timelag_atlas.gp
+        gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n|␤|g')
+        for tabfile in analyses/tables/timelag_*${errtype}*;
+        do
+            ref_band_extracted=$(basename $tabfile|sed 's|timelag_\([^≺]*\)[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*}.tab|\1|')
+            echo_band=$(basename $tabfile|sed 's|timelag_[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}.tab|\1|')
+            if [[ "$echo_band" == "$ref_band" ]] ; then continue; fi
+            gnuplot_input_edit=$(echo "$gnuplot_input"|
+                                    sed "s|%FILE%|$tabfile|"|
+                                    sed "s|%LABEL%|$echo_band|")
+            gnuplot_input="${gnuplot_input_edit}"
+        done
+        echo "$gnuplot_input"|perl -pe 's|␤|\n|g' > ${gnuplot_file}
+        gnuplot $gnuplot_file
+    ;;
+    default)
+        echo "Did not understand plot type."
+    ;; 
+esac

scripts/extract_tables.pl

@@ -1,5 +1,8 @@
 #!/usr/bin/env perl
 
+# This extracts the gnuplot-ready tables from a psdlag analysis and saves them
+# to temporary files. propogate_tables.sh uses this script to create the
+# tables it saves to analyses/tables.
 
 use utf8;
 use Encode qw(encode decode);

scripts/plot_psdlag.sh

@@ -42,7 +42,7 @@ do
 
     # Output curves to temporary files using perl script, move tables to
     # permanent location. This just assumes there are no conflicts.
-    scripts/create_tables.pl $analysis > /dev/null
+    scripts/extract_tables.pl $analysis > /dev/null
     mv tmp.echoPSD $echoPSD_tabfile
     mv tmp.refPSD $refPSD_tabfile
     mv tmp.timelag $timelag_tabfile

scripts/templates/psd_freq.gp

@@ -1,29 +1,34 @@
 # This method assumes y values are in logarithm units already.
 
-set terminal pngcairo
+set terminal pdf
 set output "%OUTPUTFILE"
-set termoption dash
+# set termoption dash
 set termopt enhanced
 
-set title "%TITLE\n{/*0.7 %SUBTITLE}"
+set title "%TITLE\n{/*0.7 %SUBTITLE}" font "Times"
-set xlabel "Temporal Frequency [days^{-1}]"
+set xlabel "Temporal Frequency [days^{-1}]" font "Times"
 set xrange [0.005:0.620]
+set xtics font "Times"
+set ytics font "Times"
 
 # Use this if you want to show PSD directly on a log axis
 # set logscale xy
-# set ylabel "PSD"
+# set ylabel "PSD" font "Times"
 # set yrange [%YMIN:%YMAX]
 # plot '%FILE1' using 1:(10**($2+2)):3:4 with xyerrorbars title "%LABEL1", \
 # '%FILE2' using 1:(10**($2+2)):3:4 with xyerrorbars title "%LABEL2"
 
 # Use this if you want to show the log value of the PSD
 set logscale x
-set ylabel "log_{10} PSD"
+set ylabel "log_{10} PSD" font "Times"
 #set yrange [%YMIN:%YMAX]
 #set yrange [-5.5:0.5]
 
 set key outside
 set key center bottom
+set key font "Times"
 
-plot '%FILE1' using 1:2:3:4 with xyerrorbars title "%LABEL1", \
+set yzeroaxis
-'%FILE2' using 1:2:3:4 with xyerrorbars title "%LABEL2"
+
+plot '%FILE1' using 1:2:3:4 with xyerrorbars title "%LABEL1" pt 0 ps 1 lt rgb "green", \
+'%FILE2' using 1:2:3:4 with xyerrorbars title "%LABEL2" pt 0 ps 1 lt rgb "red"

scripts/templates/timelag_compare.gp

@@ -2,7 +2,6 @@ set terminal pngcairo
 set termoption dash
 set termopt enhanced
 set output "%OUTPUTFILE"
-set encoding utf8
 
 set title "%TITLE\n{/*0.7 %SUBTITLE}"
 set xlabel "Temporal Frequency [days^{-1}]"